Hi Evans, Thank you very much for the suggestions! I'll post my data on an online file sharing system from now on.
Xiao On Tue, Jan 13, 2015 at 5:21 AM, Phil Evans <p...@mrc-lmb.cam.ac.uk> wrote: > It is hard to tell without having the unmerged data (don't post that to > the BB), but running the data through Pointless, Aimless ctruncate (though > I had to fix Aimless) suggests > > 1. the data are not very good > 2. the space group may be C2 > 3. it may be twinned (or just some spot overlap with the long 288A c axis) > > Phil > > On 13 Jan 2015, at 00:34, Xiao Lei <xiaolei...@gmail.com> wrote: > > > Hi Eleanor, > > > > Thank you for the advice. The .sca file is here. The data may not be > useful as you said, but the anisotropic analysis for this data is > confusing. From the phenix xtriage output, it seems the data has no > anisotropic issue (I may interpret wrong the log file, I attach part of the > xtriage log file here). But from CCP4, I know the data has anisotropic > problem (Negative Eigenvalues). > > > > Below is part of log file from Phenix. > > > > ---------------- Anisotropy analyses ---------------- > > > > Anisotropy ( [MaxAnisoB-MinAnisoB]/[MaxAnisoB] ) : 3.233e-01 > > Anisotropic ratio p-value : 0.000e+00 > > > > The p-value is a measure of the severity of anisotropy as observed > in the PDB. > > The p-value of 0.000e+00 indicates that roughly 100.0 % of datasets > available in the PDB have > > an anisotropy equal to or worse than this dataset. > > > > Xiao > > > > On Sun, Jan 11, 2015 at 7:51 AM, Eleanor Dodson < > eleanor.dod...@york.ac.uk> wrote: > > Well - I really need to see the output.sca file with the reflection list > to test the problem properly, but this log file does show your reflections > at the highest resolution are very weak, and maybe not useful. Try cutting > the resolute a bit and see what happens. > > Eleanor > > > > On 11 January 2015 at 00:08, Xiao Lei <xiaolei...@gmail.com> wrote: > > Hi Eleanor, > > > > Thanks for the input, I attach the scale log file here. > > > > On Sat, Jan 10, 2015 at 2:16 PM, Eleanor Dodson < > eleanor.dod...@york.ac.uk> wrote: > > Certainly a negative eigen value is bad - can you attach the data? There > may be some obvious problem.. > > Eleanor > > > > On 10 January 2015 at 04:42, Xiao Lei <xiaolei...@gmail.com> wrote: > > Dear All, > > > > I tried to convert my x-ray diffraction sca data from HKL200 (.sca file) > to mtz in CCP4 using Scalepack2mtz and it failed, I do not know what should > I supposed to do next to correct the problem, any suggestions are > appreciated. I pasted the message from part of log file below: > > > > > > ANISOTROPY ANALYSIS (using intensities): > > > > > > Eigenvalues: -0.5668 0.1479 0.3584 > > > > Eigenvalue ratios: -1.5815 0.4128 1.0000 > > > > ctruncate: Anisotropy correction failed - negative eigenvalue. > > > > Times: User: 0.4s System: 0.0s Elapsed: 0:00 > > > > > *************************************************************************** > > > > * Information from CCP4Interface script > > > > > *************************************************************************** > > > > The program run with command: /Applications/ccp4-6.4.0/bin/ctruncate > -hklin "/LAB/CCP4/TEMP/RelADD_12212014ALS502_3_1_mtz.tmp" -hklout > "/LAB/CCP4/TEMP/RelADD_12212014ALS502_3_3_mtz.tmp" -colin > "/*/*/\[IMEAN,SIGIMEAN\]" -colout P1_12 > > > > has failed with error message > > > > ctruncate: Anisotropy correction failed - negative eigenvalue. > > > > ObjectCache: Leaked 0005 refs to > > > > > *************************************************************************** > > > > > > > > #CCP4I TERMINATION STATUS 0 " ctruncate: Anisotropy correction failed - > negative eigenvalue. ObjectCache: Leaked 0005 refs to > > > > " > > > > #CCP4I TERMINATION TIME 09 Jan 2015 19:55:50 > > > > #CCP4I MESSAGE Task failed > > > > > > > > > > > > > > <P1_12_P1_rej2.6_output.sca> >
